While the proper selection of splice sites is essential for genomic diversity, adaptive growth and development, errors in splicing can have enormous detrimental effects on function and are now recognized as the underlying cause for many human diseases. Indeed, splicing errors are associated with muscular dystrophy, Alzheimer's disease, parkinsonism, psychiatric disorders, ataxias and cancers making the study of factors that control splice-site selection vitally important for human disease. Splicing occurs at the spliceosome, a macromolecular complex composed of several RNAs and numerous proteins. Critical to normal gene splicing is the proper selection of the 5' and 3' splice sites, events that occur early in the development of the spliceosome and whose specificity is guided by an essential family of splicing factors known as SR proteins. The phosphorylation states of SR proteins directly impact their subcellular localization and splicing activities but our understandig of how these different forms are attained is, at best, incomplete. SR protein nuclear entry and splicing function are driven by a basal level of phosphorylation (hypo-phosphorylation) catalyzed by the SRPK family of protein kinases. However, this simple paradigm of one kinase-one substrate is now being challenged as a second protein kinase family has emerged as critical SR protein regulators. The Clk family of kinases can increase SR protein phosphoryl content to a greater extent than the SRPKs, generating hyper-phosphorylated forms that are largely uncharacterized at both structural and functional levels. While they differ substantially from the SRPKs in several ways, most importantly, Clk kinases possess an additional noncatalytic domain that we showed recently is responsible for its unique hyper-phosphorylating activity. Despite its significance in controlling SR protein function and splicing, little is known about the Clk enzymes. Using novel phosphate mapping and structural techniques combined with cell-based assays, we will investigate how the Clk kinases hyper-phosphorylate SR proteins and modulate splicing.